Problem
It is due to catastrophic backtracking. Let me show where it happens, by simplifying the regex to a regex which matches a subset of the original regex:
^[^\W_*]+((\.?[\w\~-]+)*\.?[^\W_*])*$
Since [^\W_*] and [\w\~-] can match [a-z], let us replace them with [a-z]:
^[a-z]+((\.?[a-z]+)*\.?[a-z])*$
Since \.? are optional, let us remove them:
^[a-z]+(([a-z]+)*[a-z])*$
You can see ([a-z]+)*, which is the classical example of regex which causes catastrophic backtracking (A*)*, and the fact that the outermost repetition (([a-z]+)*[a-z])* can expand to ([a-z]+)*[a-z]([a-z]+)*[a-z]([a-z]+)*[a-z] further exacerbate the problem (imagine the number of permutation to split the input string to match all expansions that your regex can have). And this is not mentioning [a-z]+ in front, which adds insult to injury, since it is of the form A*A*.
Solution
You can use this regex to validate the string according to your conditions:
^(?=[a-zA-Z0-9])[a-zA-Z0-9_~-]++(\.[a-zA-Z0-9_~-]++)*+(?<=[a-zA-Z0-9])$
As Java string literal:
"^(?=[a-zA-Z0-9])[a-zA-Z0-9_~-]++(\\.[a-zA-Z0-9_~-]++)*+(?<=[a-zA-Z0-9])$"
Breakdown of the regex:
^ # Assert beginning of the string
(?=[a-zA-Z0-9]) # Must start with alphanumeric, no special
[a-zA-Z0-9_~-]++(\.[a-zA-Z0-9_~-]++)*+
(?<=[a-zA-Z0-9]) # Must end with alphanumeric, no special
$ # Assert end of the string
Since . can't appear consecutively, and can't start or end the string, we can consider it a separator between strings of [a-zA-Z0-9_~-]+. So we can write:
[a-zA-Z0-9_~-]++(\.[a-zA-Z0-9_~-]++)*+
All quantifiers are made possessive to reduce stack usage in Oracle's implementation and make the matching faster. Note that it is not appropriate to use them everywhere. Due to the way my regex is written, there is only one way to match a particular string to begin with, even without possessive quantifier.
Shorthand
Since this is Java and in default mode, you can shorten a-zA-Z0-9_ to \w and [a-zA-Z0-9] to [^\W_] (though the second one is a bit hard for other programmer to read):
^(?=[^\W_])[\w~-]++(\.[\w~-]++)*+(?<=[^\W_])$
As Java string literal:
"^(?=[^\\W_])[\\w~-]++(\\.[\\w~-]++)*+(?<=[^\\W_])$"
If you use the regex with String.matches(), the anchors ^ and $ can be removed.
Test Case 1: aB78. Result: FailTest Case 2: aB78..ab Result: FailTest Case 3: abcdef Result: PassTest Case 4: aB78,1 Result: FailTest Case 5: aB78 abc Result: Fail